Software Engineering as Instrumentation for the Long Tail of Scientific Software

The vast majority of the long tail of scientific software, the myriads of tools that implement the many analysis and visualization methods for different scientific fields, is highly specialized, purpose-built for a research project, and has to rely on community uptake and reuse for its continued development and maintenance. Although uptake cannot be controlled over even guaranteed, some of the key factors that influence whether new users or developers decide to adopt an existing tool or start a new one are about how easy or difficult it is to use or enhance a tool for a purpose for which it was not originally designed. The science of software engineering has produced techniques and practices that would reduce or remove a variety of barriers to community uptake of software, but for a variety of reasons employing trained software engineers as part of the development of long tail scientific software has proven to be challenging. As a consequence, community uptake of long tail tools is often far more difficult than it would need to be, even though opportunities for reuse abound. We discuss likely reasons why employing software engineering in the long tail is challenging, and propose that many of those obstacles could be addressed in the form of a cross-cutting non-profit center of excellence that makes software engineering broadly accessible as a shared service, conceptually and in its effect similar to shared instrumentation.Comment: 4 page

Decreasing drug development timeline via upstream process intensification

Decreasing drug development timeline via upstream process intensification A scalable, high-intensity perfusion process was developed at Boehringer Ingelheim, Fremont Inc which is 10x more productive for producing recombinant proteins than comparative fed batch processes in the same 14-day run duration. By eliminating wasteful cell bleed we were able to achieve cell densities up to five times greater than standard “steady state” perfusion culture previously used. In order to sustain such large cell masses at manageable media exchange rates, concentrated media feeds were developed which effectively allow for optimization of nutrient delivery and dilution rate. We believe this system is scalable up to 1kL; the process has already been demonstrated successfully at the pilot scale (100L), where bioreactor productivities averaging over 5 g/L/day have been demonstrated. We begin development with new cell lines for the high intensity perfusion process by adapting spin-tube and shake flask models that others have used for fed batch. These methods are used to test for important control parameters to allow full development in a 2L bioreactor. AMBR250 bioreactors can be used, though not optimal, as will be discussed. Due to the simplicity of the process design, the integrated downstream is developed at small scale using classical batch chromatographic techniques, including high throughput process development and standard chromatographic steps. The virus inactivation step is developed by accounting for viscosity and titration of the product and buffer in the Protein A elution peak, which differ slightly from product to product. With these simple development techniques, we believe the highly productive process could be commercially viable at Phase I, with limited to no Phase III process development

Workshop 3: Business Cases for Integrated and Continuous Biomanufacturing

No Abstract

Safety issues for women experiencing intimate partner violence (IPV): An integrative review

This integrative literature review examines the safety issues for women experiencing intimate partner violence (IPV) in Australian studies. Using clear inclusion and exclusion criteria, seven data bases were systematically searched for the study. A total of 10 samples were identified as suitable for the study after a thorough screening of accessed sources. For ensuring the quality and appropriateness of the sources, the CRAAP test, which examined the currency, relevance, authority, accuracy, and purpose was conducted. A thematic analysis was employed for analysing the data. Four core themes were identified from the analysis, which are: lack of IPV education and training, issues with services, systemic issues, and issues with protection orders. Together, the findings suggest how a range of social processes impact the safety of women experiencing IPV. It necessitates a holistic approach to IPV if women’s safety is to be effectively addressed.  It is vital to look at the many layers that impact women's safety rather than a focus on the individuals involved

Letter From Daisie Wagner to Alfred L. Shoemaker, March 11, 1949

A handwritten letter from Daisie Wagner addressed to Alfred L. Shoemaker, dated March 11, 1949. Within, Wagner discusses her family\u27s almanac and the figure of a man surrounded by the Zodiac signs that perplexed her as a child, along with providing an almanac rhyme in Pennsylvania-Dutch.https://digitalcommons.ursinus.edu/shoemaker_documents/1037/thumbnail.jp

Gambling among university sport students: a preliminary analysis

The aim of this study was to explore risks associated with the gambling habits and attitudes of sport students governed by betting integrity rules. Using focus groups with male and female student rugby and football players, we identified four areas of concern. First, participants considered gambling as a ‘normal’ pastime – a largely harmless form of communal entertainment. Second, we found that participants’ gambling behaviour was influenced by marketing strategies and by peers. Third, although participants were aware of some of the potential risks of gambling, they had a limited understanding of how problem gambling and addiction might develop. Taken together, we believe these encourage gambling and increase risks of gambling related problems. The fourth concern relates to breaking integrity rules. Although we found no evidence of intentional corrupt behaviour, participants had a casual attitude towards gambling regulations, and some broke the betting rules in ways they deemed trivial. Moreover, participants did not seem to take anti-corruption education/intervention particularly seriously

Progress on Infinite Cluster Categories Related to Triangulations of the (Punctured) Disk

In this mostly expository paper, we present recent progress on infinite (weak) cluster categories that are related to triangulations of the disk, with and without a puncture. First we recall the notion of a cluster category. Then we move to the infinite setting and survey recent work on infinite cluster categories of types $\mathbb{A}$ and $\mathbb{D}$. We conclude with our contributions, two infinite families of infinite (weak) cluster categories of type $\mathbb{D}$. We first present a discrete, infinite version of Schiffler's combinatorial model of the punctured disk with marked points. We then produce each (weak) cluster category starting with representations of thread quivers, taking the derived category, and then taking the appropriate orbit category. We show that the combinatorics in the (weak) cluster categories match with the corresponding combinatorics of the punctured disk with countably-many marked points. We also state two conjectures concerning weak cluster structures inside our (weak) cluster categories.Comment: 30 pages, 18 figures. For the special JAA issue on Cluster Algebras and Related Topic

Multimodal Investigation of Neuronal Responses

This thesis describes an investigation of neuronal responses with both magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI). MEG and fMRI are widely used in neuroscience. However, aspects of the MEG and fMRI signal are still not well understood, particularly post-stimulus responses – responses which occur after a stimulus has ended. Post-stimulus responses have been shown to correlate with various illnesses and as a result, MEG and fMRI have yet to reach their full potential clinically. By developing carefully controlled experiments, MEG is used in this thesis to characterise post-stimulus responses to a grip-force task. The results showed that the beta-band post-stimulus response (post-movement beta rebound, PMBR) is modulated by task duration. Functional network analysis, using amplitude envelope correlation and a hidden Markov model, showed that the PMBR re-establishes networks after breaking down during a task, suggesting the PMBR is related to functional connectivity. The results of this thesis provide new information about the nature of the PMBR, demonstrating that it can be systematically controlled by task parameters and provides insight into its generation. It is hoped this research will contribute to a deeper understanding of the PMBR and provide a step forward for its use clinically. In fMRI, the origin of the post-stimulus response is also poorly understood. To investigate fMRI post-stimulus responses, an MR pulse sequence was developed and optimised to measure blood flow, volume and oxygenation changes simultaneously at 7 T. This was implemented with the grip-force task, allowing direct comparison between MEG and fMRI. This study provides new insights into the fMRI post-stimulus undershoot which warrant further investigation. Understanding the link between fMRI and MEG signals will help further understanding of both modalities and how they relate to neuronal activity. Finally, the applications of fMRI were explored by comparing fMRI responses in patients with focal hand dystonia (FHD) with healthy controls. 7 T fMRI was used to map cortical fingertip representations and measures were developed to compare overlap of digit representations between patients and healthy controls. This project provided an important opportunity to advance the understanding of FHD and was the first study to use fMRI to explore the effects of treatment on patients with FHD